As a practiser of genealogy, I am also familiar with this phenomenon. The further you go back in time, the more often you see this occurring. It most often happens in the church books, from when civil registration (which Napoleon introduced) didn't exist yet.

I find it interesting, though, that this mostly happens with feminine names - especially with the most common ones. Anna, Maria and Joanna were the most popular feminine names in my country in at least the last three centuries. If a woman was named AnnaMaria [surname], she would often get mentioned as only Anna [surname], or Maria [surname] or as MariaAnna [surname]. I won't even start on the nicknames that were sometimes written down instead of the legal name. And in the case of a woman named Joanna, she will often be mentioned as just Anna as well.Because of that, I think those common names are a real pain when you have to identify the parents of someone with such a common name (especially when the surname is very common as well). After all, because the name is so common, you will find that there are more married couples that can be the potential parents of a person. At least with a name like Judith or Thecla it is much easier to identify a person's parents.

For the men, Joannes (later Johannes became a more common spelling) was most common and the name often gives the same problems as Anna, Maria and Joanna for the women. But at least masculine names are more stable, as their names tend to be written down correctly more often. Maybe that's because people back then thought that women weren't worth the effort (you especially see that in the church books, where the surname of the mother is often omitted in the baptism records).Anyway, a man named JoannesMathias will often be mentioned as such. If not, he will usually be mentioned by his middle name (and a man's middle name is usually less common) - or his first name, which is just a little bit less common. Then there's also the fact that women were given more often a middle name than men (AnnaCatharina, AnnaElisabeth, AnnaMargaretha, etc.), so that means that with men, there is less room for using the first and middle names interchangeably.

So, I suppose you could say that parents were more imaginative with naming their sons than they were with their daughters - because men were considered superior to women, after all. Because of that (and the reasons stated earlier), men will always be easier to work with in genealogy than women (when it comes to identifying their parents, for example). At least, in my opinion. :)